Has anyone set up chart of accounts for a coffee roasting/wholesale company? Do I need a unique sales item for each package size of the same coffee variety?

If you only need to manage a small number of sales product variations, you can do that. But you'll be adjusting your inventory manually and it might be a headache later. The built-in inventory features in QBO are limited. When you need unit of measure and matrix inventory feature, you'll need an additional app.

You may have 2 or more company files at no additional cost to manage on QB Desktop. You can run QB Desktop separately on each location or set up a simple private cloud solution to allow the second location to access file(s) at the first location via the internet.